(a) Module matching. Green, yellow, blue, and grey nodes correspond to modules in S. cerevisiae, S. pombe, C. elegans, and D. melanogaster respectively. The size of a node corresponds to the number of genes in the module. The width of an edge connecting two nodes reflects the p-value of the reciprocal match between two modules, when more significant matches correspond to wider edges. (see Additional File 13 for complete listing). (b-d) Examples for matched modules across S. cerevisiae, S. pombe, C. elegans, and D. melanogaster. Each row contains modules that significantly overlap based on orthology for all pairwise comparison. The examples are marked in a red circle in Figure 4a. The nodes are colored with the same color scheme of 4a. The edges are colored based on the interaction type (see legend - note that GI edges refer to both positive GI and negative GI edges), and multiple edges between two nodes are allowed. For clarity, only genes that have orthologs in at least one of the other modules are shown. See text for details on the matched modules.